Linear Plot Navigation Guide

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Understanding the Plot

  • Track 1 (Gene Quality): Shows genes colored by assembly quality
    • Green (Excellent): ≥95% identity
    • Yellow (Good): 85-95% identity
    • Orange (Fair): 70-85% identity
    • Red (Poor): <70% identity
  • Track 2 (Contig Mapping): Shows which assembly contigs map to the reference
  • Track 3 (Coverage Depth): Shows how many times each position is covered
  • Track 4 (Alignment Identity): Shows sequence identity percentage across the genome
  • Track 5 (Misassemblies): Highlights regions with assembly errors
    • Bottom layer: Contig positions (colored bars showing which contig)
    • Upper layers: Overlaps, Gaps, and Inversions

Interactive Features

  • Click on genes in Track 1 to view detailed alignments
  • Hover over any element to see detailed information
  • Zoom: Click and drag to select a region, double-click to reset
  • Pan: Use the pan tool in the toolbar